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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 2 callersFunctionhts_opt_free

* Frees an hts_opt list. */

src/utils/htslib/hts.c:671

↓ 2 callersFunctionhts_parse_opt_list

* Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could

src/utils/htslib/hts.c:692

↓ 2 callersFunctionhts_readlist

src/utils/htslib/hts.c:1166

↓ 2 callersFunctionhts_set_log_level

src/utils/htslib/hts.c:2945

↓ 2 callersFunctionhts_tpool_next_result_locked

Core of hts_tpool_next_result() */

src/utils/htslib/thread_pool.c:131

↓ 2 callersFunctionhts_tpool_process_empty

* Returns true if there are no items in the process results queue and * also none still pending. */

src/utils/htslib/thread_pool.c:240

↓ 2 callersFunctionhts_tpool_process_reset

* Resets a process to the initial state. * * This removes any queued up input jobs, disables any notification of * new results/output, flushes what

src/utils/htslib/thread_pool.c:867

↓ 2 callersFunctionhts_tpool_size

* Returns the number of requested threads for a pool. */

src/utils/htslib/thread_pool.c:709

↓ 2 callersFunctionhts_useek

src/utils/htslib/hts.c:1121

↓ 2 callersFunctionidx_write_uint32

src/utils/htslib/hts.c:1655

↓ 2 callersFunctioninflate_gzip_block

src/utils/htslib/bgzf.c:606

↓ 2 callersMethodinit

src/utils/NewChromsweep/CloseSweep.cpp:190

↓ 2 callersFunctionint32_encode

* Encodes a 32-bit little endian value 'val' and writes to fd. * * Returns the number of bytes written on success * -1 on failure */

src/utils/htslib/cram/cram_io.c:502

↓ 2 callersMethodisCram

src/utils/Contexts/ContextBase.h:158

↓ 2 callersFunctionisHeaderLine

src/utils/general/ParseTools.cpp:94

↓ 2 callersMethodisValidColumnOps

src/utils/KeyListOps/KeyListOps.cpp:92

↓ 2 callersMethodisZeroBased

src/utils/FileRecordTools/Records/Record.h:78

↓ 2 callersFunctionis_directory

src/utils/htslib/cram/files.c:48

↓ 2 callersMethodis_open

src/utils/gzstream/gzstream.h:64

↓ 2 callersFunctionkbs_bitwise_or

Bitwise OR, dst will be modified, src will be left unchanged

src/utils/htslib/bcf_sr_sort.c:66

↓ 2 callersFunctionkbs_clear

Reset the bit set to empty.

src/utils/htslib/htslib/kbitset.h:95

↓ 2 callersFunctionkbs_resize

Resize a bit set.

src/utils/htslib/bcf_sr_sort.c:39

↓ 2 callersFunctionkf_betai_aux

Regularized incomplete beta function. The method is taken from * Numerical Recipe in C, 2nd edition, section 6.4. The following web * page calculate

src/utils/htslib/kfunc.c:150

↓ 2 callersFunctionkf_betai_aux

Regularized incomplete beta function. The method is taken from * Numerical Recipe in C, 2nd edition, section 6.4. The following web * page calculate

src/fisher/kfunc.cpp:123

↓ 2 callersFunctionkftp_connect

src/utils/htslib/knetfile.c:280

↓ 2 callersFunctionkftp_connect_file

place ->fd at offset off

src/utils/htslib/knetfile.c:329

↓ 2 callersFunctionkhash_str2int_has_key

* Returns 1 if key exists or 0 if not */

src/utils/htslib/htslib/khash_str2int.h:66

↓ 2 callersFunctionkhttp_connect_file

src/utils/htslib/knetfile.c:414

↓ 2 callersFunctionkmemmem

src/utils/htslib/kstring.c:321

↓ 2 callersFunctionknet_win32_init

In windows, the first thing is to establish the TCP connection. */

src/utils/htslib/knetfile.c:144

↓ 2 callersFunctionkputl

src/utils/htslib/htslib/kstring.h:215

↓ 2 callersFunctionle_to_u64

Get a uint64_t value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 64 bit unsigned integer * T

src/utils/htslib/htslib/hts_endian.h:150

↓ 2 callersMethodlessThan

src/utils/FileRecordTools/Records/Record.cpp:81

↓ 2 callersFunctionlibcurl_open

src/utils/htslib/hfile_libcurl.c:1079

↓ 2 callersFunctionlinks_help

src/linksBed/linksMain.cpp:103

↓ 2 callersFunctionload_block_from_cache

src/utils/htslib/bgzf.c:661

↓ 2 callersFunctionload_ref_portion

* Used by cram_ref_load and cram_ref_get. The file handle will have * already been opened, so we can catch it. The ref_entry *e informs us * of whet

src/utils/htslib/cram/cram_io.c:2309

↓ 2 callersFunctionltf8_decode_crc

src/utils/htslib/cram/cram_io.c:373

↓ 2 callersFunctionmap_find

* Quick and simple hash lookup for cram_map arrays */

src/utils/htslib/cram/cram_decode.c:1922

↓ 2 callersFunctionmaskfastafrombed_help

src/maskFastaFromBed/maskFastaFromBedMain.cpp:127

↓ 2 callersFunctionmd5_print

src/utils/htslib/cram/cram_decode.c:2191

↓ 2 callersFunctionmfflush

* Flushes an mFILE. If this is a real open of a file in write mode then * mFILE->fp will be set. We then write out any new data in mFILE since the *

src/utils/htslib/cram/mFILE.c:594

↓ 2 callersFunctionmfload

* Reads the entirety of fp into memory. If 'fn' exists it is the filename * associated with fp. This will be used for more optimal reading (via a *

src/utils/htslib/cram/mFILE.c:74

↓ 2 callersFunctionmfreopen

* Converts a FILE * to an mFILE *. * Use this for wrapper functions to turn external prototypes requring * FILE * as an argument into internal code

src/utils/htslib/cram/mFILE.c:255

↓ 2 callersFunctionmp_alloc

src/utils/htslib/sam.c:2248

↓ 2 callersFunctionmt_destroy

src/utils/htslib/bgzf.c:1431

↓ 2 callersFunctionmt_queue

src/utils/htslib/bgzf.c:1458

↓ 2 callersFunctionmultiDbOutputHelp

src/utils/general/CommonHelp.cpp:91

↓ 2 callersFunctionmultibamcov_help

src/multiBamCov/multiBamCovMain.cpp:147

↓ 2 callersFunctionmy_netread

src/utils/htslib/knetfile.c:192

↓ 2 callersMethodname

src/utils/BamTools/mapping/BamAlignment.py:5

↓ 2 callersFunctionnuc_help

src/nucBed/nucBedMain.cpp:121

↓ 2 callersFunctionopen_nextdir

src/utils/htslib/plugin.c:42

↓ 2 callersFunctionpackInt16

src/utils/htslib/bgzf.c:157

↓ 2 callersFunctionpairtobed_help

src/pairToBed/pairToBedMain.cpp:171

↓ 2 callersFunctionpairtopair_help

src/pairToPair/pairToPairMain.cpp:149

↓ 2 callersFunctionparse_ini

src/utils/htslib/hfile_s3.c:169

↓ 2 callersFunctionparse_version

Parse "x.y" text, taking care because the string is not NUL-terminated and filling in major/minor only when the digits are followed by a delimiter, so

src/utils/htslib/hts.c:158

↓ 2 callersMethodprintClosest

src/utils/RecordOutputMgr/RecordOutputMgr.cpp:155

↓ 2 callersFunctionprint_record

src/utils/FileRecordTools/Records/Bed6Interval.cpp:26

↓ 2 callersFunctionprint_record

src/utils/FileRecordTools/Records/BedGraphInterval.cpp:23

↓ 2 callersFunctionprint_record

src/utils/FileRecordTools/Records/Bed5Interval.cpp:24

↓ 2 callersFunctionprint_record

src/utils/FileRecordTools/Records/Bed3Interval.cpp:35

↓ 2 callersFunctionpriority

src/utils/htslib/hfile.c:976

↓ 2 callersFunctionprobaln_glocal

The topology of the profile HMM: /\ /\ /\ /\ I[1] I[k-1] I[k] I[L]

src/utils/htslib/probaln.c:75

↓ 2 callersFunctionrandom_help

src/randomBed/randomBedMain.cpp:107

↓ 2 callersFunctionrans_compress_O0

src/utils/htslib/cram/rANS_static.c:69

↓ 2 callersFunctionrans_uncompress

src/utils/htslib/cram/rANS_static.c:770

↓ 2 callersFunctionrealloc_bam_data

src/utils/htslib/sam.c:314

↓ 2 callersFunctionrealn_check_tag

src/utils/htslib/realn.c:89

↓ 2 callersFunctionrefs_load_fai

* Loads a FAI file for a reference.fasta. * "is_err" indicates whether failure to load is worthy of emitting an * error message. In some cases (eg w

src/utils/htslib/cram/cram_io.c:1623

↓ 2 callersFunctionregidx_init

src/utils/htslib/regidx.c:169

↓ 2 callersFunctionregidx_insert

src/utils/htslib/regidx.c:119

↓ 2 callersFunctionreldist_help

src/reldist/reldistMain.cpp:114

↓ 2 callersFunctionremove_vset

src/utils/htslib/bcf_sr_sort.c:205

↓ 2 callersMethodreportToFileBedNewLine

src/utils/bedFile/bedFile.h:1010

↓ 2 callersFunctionrestart_from_position

src/utils/htslib/hfile_libcurl.c:898

↓ 2 callersFunctions3_rewrite

src/utils/htslib/hfile_s3.c:310

↓ 2 callersFunctionsam_hdr_PG_ID

* Returns a unique ID from a base name. * * The value returned is valid until the next call to * this function. */

src/utils/htslib/cram/sam_header.c:1161

↓ 2 callersFunctionsam_hdr_length

src/utils/htslib/cram/sam_header.c:1064

↓ 2 callersFunctionsam_hdr_parse

src/utils/htslib/sam.c:898

↓ 2 callersFunctionsam_hdr_rebuild

* Reconstructs the kstring from the header hash table. * Returns 0 on success * -1 on failure */

src/utils/htslib/cram/sam_header.c:793

↓ 2 callersFunctionsam_hdr_sort_order

* Returns the sort order: */

src/utils/htslib/cram/sam_header.c:757

↓ 2 callersFunctionsam_hdr_update

* Adds or updates tag key,value pairs in a header line. * Eg for adding M5 tags to @SQ lines or updating sort order for the * @HD line (although use

src/utils/htslib/cram/sam_header.c:710

↓ 2 callersFunctionsam_hdr_update_hashes

Updates the hash tables in the SAM_hdr structure. * * Returns 0 on success; * -1 on failure */

src/utils/htslib/cram/sam_header.c:98

↓ 2 callersFunctionsam_index_build3

src/utils/htslib/sam.c:606

↓ 2 callersMethodsameChromIntersects

src/utils/FileRecordTools/Records/Record.cpp:150

↓ 2 callersFunctionsanitise_SQ_lines

* Verifies that the CRAM @SQ lines and .fai files match. */

src/utils/htslib/cram/cram_io.c:1765

↓ 2 callersMethodsequenceLength

src/utils/Fasta/Fasta.cpp:142

↓ 2 callersMethodset

src/utils/general/QuickString.cpp:233

↓ 2 callersMethodsetDBfileType

src/utils/KeyListOps/KeyListOps.h:48

↓ 2 callersMethodsetDelimStr

src/utils/KeyListOps/KeyListOps.h:36

↓ 2 callersMethodsetFileType

src/utils/bedFile/bedFile.cpp:652

↓ 2 callersMethodsetFilesPerRun

src/regressTest/RegressTest.h:27

↓ 2 callersMethodsetInHeader

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:35

↓ 2 callersMethodsetIoBufSize

src/utils/FileRecordTools/FileRecordMgr.h:107

↓ 2 callersMethodsetIsGroupBy

src/utils/FileRecordTools/FileRecordMgr.h:109

↓ 2 callersMethodsetKeepFinalIncompleteElem

src/utils/general/Tokenizer.cpp:107

↓ 2 callersMethodsetNullValue

src/utils/KeyListOps/KeyListOps.h:35

↓ 2 callersMethodsetNumFields

src/utils/FileRecordTools/Records/GffRecord.h:32

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